[BioC] unwrapdups for duplicate spots on custom array

Naomi Altman naomi at stat.psu.edu
Wed Mar 8 21:40:19 CET 2006

What I would do is to normalize the data and then sort by geneid.
Once it is sorted, you can used spacing=1.

Does this make sense?  It depends on whether the correlation is 
related to distance (bad) or just to array (OK).


At 09:36 AM 3/8/2006, Steffen Neumann wrote:
>[This is a repost of a message sent 20hrs ago, which didn't appear
>  on the list -- apologies if you received this twice.]
>I am currently working on the analysis of the SGED Study 073,
>which has been performed with the potato_10K_v3_sep14_2004 chip,
>I found that the pattern for replicated spots is non-trivial,
>duplicates are within a block, but with the upper-left spots
>duplicated in the lower right of a block, and lower left spots
>replicated on the upper right.
>The spacing is 220 for spots in the rectangle (1,1) through (13,18)
>and 455 for spots in (14,1) to (26,8). A plot of the pairs
>is available at msbi.ipb-halle.de/~sneumann/lines.pdf
>I'd like to use calculate the duplicateCorrelation and do an lmFit.
>Should I
>        1) hack unwrapdups to understand this/any layout
>        2) hack/rearrange the inputfiles, possibly with side-effects
>           for the normalization (?!)
>        3) Do something completely different ?
>Checking the Archive I found very few references to duplicates
>which are not "columns" , "rows" or "topbottom". Did I miss something ?
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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